Towards the end of the Clone Wars, Black Sun's leader Ziton Moj proposed merging with the Pyke Syndicate, which specialized in distributing illegal narcotics. When the Pyke leader Marg Krim rejected his demands, Moj retaliated by kidnapping his family in order to force Krim to change his mind. Krim then hired two independent bounty hunters—the former Sith apprenticeAsajj Ventress and the undercover Jedi MasterQuinlan Vos—to rescue his family. The two bounty hunters raided the Black Sun fortress on Mustafar and succeeded in rescuing Krim's family. During the rescue mission, Moj and his Falleen guards were assaulted by Ventress and Vos. Black Sun retaliated by sending a fleet to attack the Pyke stronghold of Oba Diah.[17]

After Palpatinetransformed the Republic into his own Galactic Empire at the end of the Clone Wars, Black Sun formed a durable relationship with the new autocratic government.[18] A year after the establishment of the Empire, Black Sun took an interest in Ahsoka Tano, one of their agents finding her and offering a job with them. When she refused, they attacked, but were driven away by Bail Organa's forces coming to her defense.[3] During the Age of the Empire, Black Sun owned a Pantolomin cruiser.[19] The former Imperial cadetsSabine Wren and Ketsu Onyo decided to join Black Sun as bounty hunters. However, Ketsu got "greedy", left her former classmate for dead, and joined Black Sun by herself. Years later, Ketsu accepted a Black Sun job to collect a GNK-series power droid called EG-86, which was carrying information vital to the rebellion. This mission brought her into conflict with Sabine but the two reconciled and joined forces to escape the Empire and to deliver the droid to the rebellion. Some rebels like Sabine despised Black Sun for engaging in slave trafficking.[11]

At the time of the New Republic's founding, Black Sun was one of several major crime syndicates operating in the Outer Rim.[20] In 5 ABY, the Black Sun BossGyuti placed a bounty on the head of the Zabrak bounty hunter Jas Emari for debts incurred by her aunt Sugi. UnderbossRynscar and her henchmen ambushed Jas and Sugi while they were visiting Nar Shaddaa for information on Han Solo's whereabouts. Jas managed to convince Rynscar not to turn her in by offering to repay them double the amount she owed. Rysncar also provided Jas with information about Han Solo's whereabouts.[8]